Edit:
According to https://www.jetbrains.com/pycharm/whatsnew/#v2016-3-venv-in-terminal, PyCharm 2016.3 (released Nov 2016) has virutalenv support for terminals out of the box
Auto virtualenv is supported for bash, zsh, fish, and Windows cmd. You
can customize your shell preference in Settings (Preferences) | Tools
| Terminal | check Activate virtaulenv
you also need to make sure to have the path of virtual environment path included in the content root folder of your project structure. You can go to settings (preference) | project | Project Structure | if your environment is not included in the project directory.
***Old Method:***
Create a file .pycharmrc
in your home folder with the following contents
source ~/.bashrc
source ~/pycharmvenv/bin/activate
Use your virtualenv path as the last parameter.
Then set the shell Preferences->Project Settings->Shell path to
/bin/bash --rcfile ~/.pycharmrc